Hi Steven
As I remember, TPI is based on the calculation of the potential at every
conformation from the already computed simulation (inserting the
particle in every snapshot), so velocities are not used.
Anyway, use both and see if there are any differences.
Javier
El 09/05/12 11:27, Steven Neumann escribió:
Dear Gmx Users,
I am running TPI of the water in the system containing free amino
acids. Steps:
1. I run the NPT simulation of 100 ns to equilibrate the system.
2. I added 1 extra water molecule to the final pdb file (converted
from gro) and to topology
3. I creaded tpi.tpr using grompp using new pdb file with extra water
molecule
4. mdrun --s tpi298.tpr -rerun md298.trr -deffnm tpi298 -tpi
tpi298.xvg -tpid tpid298.xvg
My question: Is it better generate new velocities in my mdp file
(continuation = yes, gen_vel = no, tpi integrator) for a pdb file or
use velocities from previous simulations (gro file)?
If the second option is more appropriate what velocity shall I adjust
to the extra water molecule?
I will appreciate your reply.
Steven
--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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